Master cylinder size is directly related to the area of the pistons. It's all hydraulic ratios really.
Basically, the smaller the bore MC you use, the softer the pedal will be. But go too small and it won't move enough fluid and you get a mushy feeling.
Stock MC is 21mm bore. This is fine for rear dums because the wheel cylinders require very little fluid to move far. Basically all you are moving is the front calipers. The smallest 4-wheel disk MC is the 94-95 Cobra MC at 15/16...or basically 24mm. The '93 Cobra MC is 25.5mm. The larger you go, the more fluid gets pushed and the stiffer the pedal becomes.
Which MC to use depends on the caliper piston area. So you can't go by someone else's setup if they are using different calipers. It really all depends on the total piston area.
Your setup with the 03 cobra front and the SVO rears is very unique. Basically, the stock Fox has 5654mm^2 of piston surface area (not including the tiny wheel cylinders in the rear) and now with the '03 Cobra fronts and SVO rears, you have 9732mm^2 of caliper piston area....so you nearly doubled it. You need to increase your MC bore proportionally to compensate.
Basically, here are the available MC's
You have the smallest right now...reason why the pedal is mushy. Either of the two largest will be fine. The GT/V6 MC will give you a hydraulic ratio of 17.0:1...which is what the 99-04 V6's are, while the SVO MC gives you a ratio of 15.2:1...which is more ideal.
Most Factory OEM setups are ina range of 13:1 to 16:1....the lower the ratio, the firmer the pedal.